Dynamic Covalent Assembly of Peptoid-Based Ladder Oligomers by Vernier Templating

Article abstract of DOI:10.1021/jacs.5b11251

Dynamic covalent chemistry, in conjunction with template-directed assembly, enables the fabrication of extended nanostructures that are both precise and tough. Here we demonstrate the dynamic covalent assembly of peptoid-based molecular ladders with up to 12 rungs via scandium(III)-catalyzed imine metathesis by employing the principle of Vernier templating, where small precursor units with mismatched numbers of complementary functional groups are coreacted to yield larger structures with sizes determined by the respective precursor functionalities. Owing to their monomer diversity and synthetic accessibility, sequence-specific oligopeptoids bearing dynamic covalent pendant groups were employed as precursors for molecular ladder fabrication. The generated structures were characterized using matrix-assisted laser desorption/ionization mass spectrometry and gel permeation chromatography, confirming successful molecular ladder fabrication.

Full text of DOI:10.1021/jacs.5b11251

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Article
Dynamic Covalent Assembly of Peptoid-
Based Ladder Oligomers by Vernier Templating
Tao Wei, Jae Hwan Jung, and Timothy F Scott
J. Am. Chem. Soc., Just Accepted Manuscript • DOI: 10.1021/jacs.5b11251 • Publication Date (Web): 07 Dec 2015
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Journal of the American Chemical Society
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Dynamic Covalent Assembly of Peptoid-Based Ladder Oli-
gomers by Vernier Templating
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Tao Wei,† Jae Hwan Jung,† and Timothy F. Scott,*,†,‡
† Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48105, US
‡ Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48105, US
ABSTRACT: Dynamic covalent chemistry, in conjunction with template-directed assembly, enables the fabrication of
extended nanostructures that are both precise and tough. Here, we demonstrate the dynamic covalent assembly of pep-
toid-based molecular ladders with up to 12 rungs via scandium(III)-catalyzed imine metathesis by employing the principle
of Vernier templating, where small precursor units with mismatched numbers of complementary functional groups are
co-reacted to yield larger structures with sizes determined by the respective precursor functionalities. Owing to their
monomer diversity and synthetic accessibility, sequence-specific oligopeptoids bearing dynamic covalent pendant groups
were employed as precursors for molecular ladder fabrication. The generated structures were characterized using matrix-
assisted laser desorption/ionization (MALDI) mass spectrometry and gel permeation chromatography (GPC), confirming
successful molecular ladder fabrication.
Despite the recent advances in self-assembly for ‘bot-
INTRODUCTION
tom-up’ construction techniques, approaches to achieve
hybridization registry between large, complementary oli-
A long-standing challenge in molecular self-assembly is
gomers and polymers have long been challenging owing
the ability to construct sophisticated yet strong nanoscale
to kinetic trapping, even for those employing non-
objects and devices with exacting structural control.
covalent interactions. Moreover, the fabrication of large
Large, naturally-occurring supramolecular structures,
structures typically requires templates of equivalent sizes,
such as viral capsids and microtubules, emerge from the
which themselves are difficult to synthesize24,25 owing to
self-assembly of relatively small subunits;1,2 however, the-
the intractability of sequence-specific polymer synthesis.26
se assembly processes are often based upon weak inter-
A recently-described self-assembly approach to address
molecular interactions such as hydrogen bonding, π-
the limitations of conventional template assembly em-
stacking, or van der Waals interactions.3 One conse-
ploys the co-reaction of oligomeric precursors with une-
quence of the relative weakness of these transient interac-
qual numbers of complementary functional groups.24-32
tions is that the assembled structures are often fragile and
This process, known as Vernier templating, results in as-
susceptible to thermal or mechanical degradation.4-6 Re-
sembled structures where each component precursor only
cently, interest in utilizing dynamic covalent chemistry
participates in as many interactions as its number of reac-
(DCC) to mediate self-assembly reactions has emerged
tive functional groups allows, whereas the total number of
because they afford error-correction mechanisms neces-
interaction sites on the Vernier complex is equal to the
sary for the selective fabrication of intricate nanostruc-
lowest common multiple of the functionality on the re-
tures while retaining the robustness of covalent bonding.
spective precursors. Thus, this templated molecular fabri-
In these dynamic covalent interactions, molecular species
cation approach curtails the kinetic trapping that would
undergo dynamic exchange and reorganization processes
otherwise impede the selective assembly of long precursor
through the reversible formation and breakage of cova-
strands and affords a facile route to the generation of
lent connections to achieve thermodynamic equilibrium.7-
large constructs from relatively small, oligomeric precur-
9
Consequently, DCC-based approaches have been uti-
sors.24-32 Implementations of Vernier templating have uti-
lized to construct a variety of macromolecular architec-
lized several different mechanisms. For example, metal-
tures, including covalent organic frameworks,10,11 macro-
ligand interactions between transition metals and por-
cycles,12-15 molecular cages,16-20 and molecular ladders and
phyrin-based oligomers have been employed to assemble
grids.21-23
a variety of structures, including triple-stranded Vernier
complexes,29 and macrocycles that, upon subsequent liga-
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tion, yielded large structures containing different num- assembly of complementary oligopeptoids with non-
bers of porphyrin units.24,30,31 Additionally, several
groups26,32 have demonstrated the Vernier-templated as-
sembly of length-programmed DNA nanostructures. No-
tably, these Vernier templating self-assembly approaches
reported to date have relied upon relatively weak inter-
molecular interactions. In contrast, the alternative ap-
proach of DCC-mediated Vernier templating provides an
avenue for the construction of large and tough assemblies
with well-defined sizes.
commensurate functionalities into molecular ladders with
m × n rungs (VA_Al×Am_m×n, where VA is ‘Vernier as-
sembly’).
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RESULTS AND DISCUSSION
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Dimerization of Complementary n×n Oligopeptoids
The rearrangement of imine bonds, generated by the
condensation of aldehyde and amine functional groups,
via imine metathesis was selected here for the self-
assembly of molecular ladders as it is a well-characterized
dynamic covalent interaction that has been extensively
applied to the synthesis of equilibrium reaction
mixtures.33 Moreover, Lewis acids have been found to effi-
ciently catalyze imine metathesis, such that the subse-
quent rapid bond rearrangement allows equilibrium to be
attained on appropriate time scales.34 Finally, the direc-
tionality of the imine bond precludes homodimerization,
enabling its utilization in the fabrication of complex,
asymmetric constructs.22 We employ scandium(III)-
catalyzed imine metathesis to mediate the dynamic cova-
lent assembly of peptoid-based molecular ladders through
both dimerization and Vernier templating by co-reacting
oligomeric precursors of commensurate and non-
commensurate lengths, respectively. To the best of our
knowledge, this work represents the first demonstration
of Vernier-templated self-assembly via DCC.
Peptoids or poly(N-substituted glycine)s, a class of pep-
tidomimetic, sequence-specific polymers35 that are readily
synthesized from a diverse range of primary amine-based
monomers, were employed here to enable the rapid pro-
totyping of precursor strands for subsequent ladder as-
sembly. Oligomeric peptoid sequences incorporating
pendant aldehyde and amine functional groups were pre-
pared using the ‘submonomer’ solid-phase peptoid syn-
thesis approach,36 where a peptoid chain is grown via se-
quential addition reactions one unit at a time using an
automated peptide synthesizer. These peptoid sequences
were synthesized as alternating co-oligomers consisting of
dynamic covalent monomer residues, utilizing monomers
bearing benzaldehyde- and aniline-based functional
groups protected with acid-labile groups to prevent un-
wanted side reactions during solid-phase synthesis, inter-
spersed with inert residues. Whereas the aldehyde and
amine functional groups allow the hybridization of com-
plementary peptoid chains through imine formation and
exchange reactions, inert residues were incorporated to
improve assembled ladder solubility. Upon cleavage from
the solid support resin and protecting group deprotection
by treatment with trifluoroacetic acid (TFA), the generat-
ed oligomeric peptoids were purified by preparative re-
verse-phase high performance liquid chromatography
(HPLC) and purity and molecular weights characterized
by analytical HPLC, NMR, and electrospray ionization
(ESI) mass spectrometry, respectively (Figures S2-S5). The
dynamic covalent reactants incorporated on the synthe-
sized peptoid oligomers were either exclusively aldehyde
or amine functional groups to avoid potential premature
aldehyde/amine condensation reactions that would pre-
clude oligomer purification. Preliminary hybridization
experiments of peptoids incorporating benzylamine or 2-
methoxyethylamine as inert spacer residues resulted in
rapid formation of a precipitate after complementary oli-
gomer mixing, indicating poor solubility of the assembled
E3AꢀAm_n
E3AꢀAl_m
(a)
O
N
O
N
O
N
O
N
O
O
O
O
O
O
O
O
O
O
O
O
H2N
N
O
N
N
nꢀ2
H2N
N
O
N
N
mꢀ2
O
O
O
O
O
NH2
NH2
NH2
(b)
(c)
NH2NH
2N
N
NH2NH2NH2NH2
Sc(OTf)3
CHCl3
N
N
N
N
+
+
NH2
N
N
N
HB_4
+
......
+
4
3
+
3
2
NH2NH2NH2
NH2NH2NH2NH2
N
N
N
N
N
N
N
NH2
N
N
N
N
N
N
NH2NH2
N
+
+
...... Intermediates
...... Intermediates
structures.
Fortunately,
utilizing
2-(2-
ethoxyethoxy)ethylamine (E3A) as the spacer residue was
found to afford solubility of both the unhybridized oligo-
mers and the subsequent assembled molecular ladders in
chloroform, and thus was employed as the alternating co-
monomer for the peptoid sequences throughout this
study. Structures of the synthesized peptoid co-oligomers
E3A-Al_m and E3A-Am_n, where m and n refer to the
number of repeat units for the aldehyde- and amine-
bearing oligomers, respectively, are shown in Scheme 1(a).
Sc(OTf)3/CHCl3
Sc(OTf)3/CHCl3
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
VA_Al×Am_m×n (m n)
Scheme 1. Dynamic covalent assembly of peptoid-based
molecular ladders. (a) Structures of linear oligopeptoids
bearing pendant amine (E3A-Am_n) and aldehyde (E3A-
Al_m) functional groups. (b) Dimerization of complemen-
tary peptoid oligomers with commensurate functionali-
ties (HB_n, where HB is ‘hybrid’). (c) Vernier-templated
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The dynamic covalent assembly of complementary oli-
the [M+Na]+ ion predominates in each of these mass spec-
tra, minor peaks attributable to [M+H]+ and [M+K]+ ions
are also observed. Peaks which could be assigned to misa-
ligned or out-of-register products, anticipated to arise at
m/z values of +18 (i.e., the molecular weight of the H2O
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gomeric peptoid sequences with commensurate lengths n
into n-rung molecular ladders was initially examined.
Here, aldehyde- and amine-functionalized peptoid se-
quences E3A-Al_m and E3A-Am_n, where m = n, were
added in a 1:1 stoichiometric ratio to chloroform with a
catalytic amount of scandium(III) triflate (Scheme 1(b))
and the reaction mixture was stirred at room temperature
overnight. No precipitate or cloudiness was observed
throughout the course of the reaction, indicating good
solubility of the resultant ladder structures and an ab-
sence of particulate, cross-linked polymer. The reaction
mixture was directly analyzed by matrix-assisted laser
desorption/ionization (MALDI) mass spectrometry, per-
formed with 2-(4-hydroxyphenylazo)benzoic acid (HABA)
as the matrix, and gel permeation chromatography (GPC)
with chloroform/methanol /triethylamine (94/4/2, v/v/v)
as the eluent. Finally, sodium triacetoxyborohydride was
added to the reaction mixture to reduce the interstrand
imine groups to secondary amines, irreversibly fixing the
assembled structures and MALDI mass spectrometry was
again performed. Attempts to characterize the reduced
molecular ladders by GPC proved unsuccessful owing to
insufficient signal intensities from both UV and differen-
tial refractive index (DRI) detectors.
condensation
product)
for
each
unreacted
amine/aldehyde pair, or to unreacted peptoid oligomers
were not observed in any of these mass spectra. Moreo-
ver, higher molecular weight species, potentially resulting
from the co-reaction of more than two peptoid strands
(i.e., (E3A-Al_m)x(E3A-Am_n)y, where m = n and x+y>2),
were not observed. Near-exclusive formation of the de-
sired ladder structures was further confirmed by GPC
chromatograms showing one major peak preceded by
very small peaks potentially attributable to low concen-
trations of higher molecular weight species (see Figure
1(b)). In each case, by comparing to low dispersity poly-
styrene standards, the elution volumes confirm the mo-
lecular weights corresponding to the resultant molecular
ladders. Furthermore, deconvolution of the experimental
GPC chromatograms revealed that the obtained molecu-
lar ladders were uniform with dispersities approaching 1
(see Figure S14 and Table S5). Interestingly, although the
GPC chromatograms suggest the presence of small
amounts of higher molecular weight, out-of-registry by-
products in the reaction mixtures, no corresponding evi-
dence for these byproducts is apparent in the MALDI
mass spectra. A previous examination of the dynamic co-
valent assembly of single-stranded precursors into n-rung
molecular ladders22 using m-phenylene-ethynylene-based
oligomers proved only moderately successful as the mo-
lecular ladder assembly became kinetically trapped at
four rungs.23 Thus, ladders containing five or more rungs
were unable to be synthesized in high yield owing to the
inadequate error-correction of misaligned, out-of-register
byproducts.23 In contrast to this previous investigation,
the success of our peptoid-based oligomer hybridization
even for 6-rung ladders, the longest examined here using
commensurate length precursor strands, suggests that the
flexibility of the peptoid backbone likely helps curtail ki-
netic trapping while the close spacing between dynamic
covalent residues affords cooperative binding, improving
hybridization selectivity and enabling formation of the
desired product. Although our utilization of peptoid oli-
gomers backbone improves upon the previously-
described approach employing m-phenylene-ethynylene
oligomers, thermodynamically disfavored but kinetically
trapped products will necessarily be generated for suffi-
ciently long precursor oligomers; thus, we investigated
Vernier templating as a facile approach to achieve large
molecular ladders from the dynamic covalent assembly of
small oligomeric species.
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Figure 1. Molecular ladders formed by dynamic covalent
oligopeptoid dimerization. (a) MALDI mass spectra of the
crude reaction mixtures. Calculated molecular weights:
[MHB_3+Na]+ = 1832.927 g/mol; [MHB_4+Na]+ = 2512.286 g/mol;
[MHB_6+Na]+ = 3871.002 g/mol. (b) GPC traces for crude reac-
tion mixtures. The traces are normalized to the height of the
largest peak. HB_3, Vr = 19.82 mL, Mn = 2270 g/mol, PDI =
1.01; HB_4, Vr = 19.37 mL, Mn = 2870 g/mol, PDI = 1.01; HB_6,
Vr = 18.87 mL, Mn = 3770 g/mol, PDI = 1.01 (polystyrene
standards).
MALDI mass spectra of the crude and reduced peptoid
dimerization reaction mixtures are shown in Figure 1(a)
and Figure S11, respectively. These mass spectra indicate
only a single product from each dimerization reaction,
where the observed dominant peaks correspond to the
desired molecular ladder structures HB_3, 4, and 6,
demonstrative of the successful formation of the desired
ladder structures which are the only reasonable products
equivalent to the observed molecular weights. Although
Vernier-templated Assembly of Complementary
m×n Oligopeptoids
The Vernier template-directed assembly of molecular
ladders was similarly investigated via application of
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Sc(III)-catalyzed metathesis of inter-strand imine bonds. length precursor strands shown in Figure 2(a) and Figure
1
2
3
4
5
6
7
8
As before, aldehyde- and amine-functionalized peptoid
oligomers were added to chloroform such that the stoi-
chiometric ratio of dynamic covalent reactants was 1:1;
however, in this case, the functionalities of the peptoids
E3A-Al_m and E3A-Am_n in the reaction mixture were
not commensurate (i.e., m ≠ n) (Scheme 1(c)). In the
presence of a catalytic amount of scandium(III) triflate,
the reaction mixture was stirred at room temperature for
one week and analyzed by both MALDI mass spectrome-
try and GPC. The self-assembly of four different oligomer
combinations were examined: VA_Al×Am_3×4 (i.e., trial-
S12, respectively, demonstrate major peaks assignable to
the desired 12-rung ladder structures with observed mo-
lecular weights equivalent to the expected values, demon-
strating the success of this dynamic covalent approach to
Vernier-templated self-assembly. Notably, in addition to
the desired product, the mass spectra also indicate the
presence of partially-assembled intermediates. For exam-
ple, mass spectra of the trimer and tetramer peptoid co-
reactions revealed peaks corresponding to partially-
assembled intermediates of (E3A-Al_3)3(E3A-Am_4)2 for
the trialdehyde/tetraamine system, and (E3A-Al_4)2(E3A-
Am_3)3 and (E3A-Al_4)2(E3A-Am_3)2 for the tetraalde-
hyde/triamine system. Similarly, for the tetramer and
hexamer peptoid co-reactions, additional peaks in the
mass spectra are assignable to the intermediate (E3A-
Al_4)2(E3A-Am_6)1 for the tetraaldehyde/hexamine sys-
tem, and (E3A-Al_6)1(E3A-Am_4)2 for the hexaalde-
hyde/tetraamine system.
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dehyde/tetraamine),
hyde/triamine),
VA_Al×Am
VA_Al×Am_4×6
_4×3
(tetraalde-
(tetraalde-
hyde/hexaamine), and VA_Al×Am_6×4 (hexaalde-
hyde/tetraamine). These combinations were selected as
each reaction was anticipated to yield 12-rung molecular
ladder products, based on the lowest common multiple of
both 3×4 and 4×6. Notably, although the ladders
VA_Al×Am_3×4 and VA_Al×Am_4×3 share the same mo-
lecular weight, and the ladders VA_Al×Am_4×6 and
VA_Al×Am_6×4 similarly share the same molecular
weight, the different numbers of E3A solubilizing groups
incorporated into the constituent peptoid strands results
in different molecular weights between the Vernier-
templated trimer/tetramer and tetramer/hexamer sys-
tems despite both yielding 12-rung molecular ladders.
Further evidence of Vernier assembly was obtained
from GPC as performed on the crude reaction mixtures
(see Figure 2(b)). Here, the multiple observed peaks cor-
respond both to the desired 12-rung molecular ladders
and to the partially-assembled intermediates. These reac-
tion mixture chromatograms were deconvoluted by au-
tomated peak fitting (see Figure S15), enabling peaks at-
tributable to the multiple species in the mixtures to be
resolved. By determining the potential structures that
could be formed during the assembly process, we as-
signed the resolved peaks to the desired Vernier ladders
and specific intermediate structures (see Tables S6-S9).
The area percentages of the desired ladder structures as
determined from GPC peak deconvolution were relatively
low (~6.5 – 14.7%, Tables S6-S9) and no correlation was
observed between the precursor oligomer lengths and the
12-rung molecular ladder yield. The resolved peaks as-
signed to the desired Vernier ladder structures exhibit
uniformity with molecular weights closely corresponding
to the expected values. However, as the partially-
assembled intermediates as determined by GPC peak de-
convolution are not wholly consistent with those present
in the MALDI mass spectra, we could not rule out the
presence of additional, out-of-registry ladder complexes.
Despite the extended reaction times and excellent registry
observed for the dimerization of complementary n×n oli-
gopeptoids, the attained mixtures, composed of the de-
sired Vernier ladders and partially-assembled intermedi-
ates, may result from sluggish strand exchange amongst
the generated molecular ladders. To further examine the
origin of this slow elimination of out-of-registry interme-
diates, we monitored the scrambling of molecular ladders
by mass spectrometry.
Figure 2. Vernier-templated assembly of molecular ladders.
(a) MALDI mass spectra of the crude reaction mixtures. The
target ladder structures are labeled with * symbols and the
intermediates are labeled with #. Calculated molecular
weights for the target ladders: [M3×4+Na]+ = [M4×3+Na]+
=
7376.810 g/mol; [M4×6+Na]+ = [M6×4+Na]+ = 7604.946 g/mol.
Intermediates are identified as (E3A-Al_3)3(E3A-Am_4)2;
(E3A-Al_4)2(E3A-Am_3)3, (E3A-Al_4)2(E3A-Am_3)2; (E3A-
Al_4)2(E3A-Am_6)1; (E3A-Al_6)1(E3A-Am_4)2. (b) GPC traces
for crude reaction mixtures (PS standards). The traces are
normalized to the height of the largest peak. The target lad-
der structures are labeled with * symbol. VA_Al×Am_3×4, Vr
= 17.78 mL, Mn = 7270 g/mol, PDI = 1.04; VA_Al×Am_4×3, Vr
= 17.81 mL, Mn = 7120 g/mol, PDI = 1.05; VA_Al×Am_4×6, Vr =
17.72 mL, Mn = 7700 g/mol, PDI = 1.06; VA_Al×Am_6×4, Vr =
17.73 mL, Mn = 7650 g/mol, PDI = 1.01.
Molecular Ladder Scrambling by Strand Exchange
The Vernier-templated assembly described here in-
volves multiple, simultaneous reactions, including tran-
simination and imine metathesis, to facilitate bond rear-
MALDI mass spectra of the crude and reduced hybridi-
zation reaction mixtures utilizing non-commensurate
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(a) E3AꢀAm_4 with ME3AꢀHB_4
rangements and yield the most thermodynamically fa-
vored products. As indicated above, in addition to the
1
2
[M′+Na]+
desired Vernier ladders, we observed the continued pres-
ence of intermediate species in the reaction mixtures even
after extended reaction times. To determine if the exist-
ence of intermediate species is a result of the respective
reactions having not reached equilibrium, we performed
kinetic studies of peptoid-based molecular ladder scram-
bling through two different approaches: transimination
between a tetraamine-bearing peptoid and a 4-rung mo-
lecular ladder (Scheme 2), and imine metathesis between
two different 4-rung molecular ladders (Scheme 3). These
tetrafunctional oligomeric species were selected because
there are at most four interactions amongst individual
strands in the Vernier assemblies. Here, we employed
precursor peptoid oligomers bearing different spacer resi-
dues such that, upon molecular ladder scrambling, mo-
lecular weights of the generated scrambled products dif-
fers from their parent molecular ladders, enabling facile
detection by MALDI mass spectrometry.23
3
4
5
6
7
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9
HB_4s
[Ms+Na]+
t = 216 h
t = 144 h
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t = 72 h
[M′+K]+
[M′+H]+
t = 0 h
2300 2400 2500 2600 2700 2800 2900
m/z
(b)
0.12
E3AꢀAm_4 with ME3AꢀHB_4
HB_4s
0.10
0.08
0.06
0.04
0.02
0
+
Sc(III)
+
+
E3AꢀAm_4 ME3AꢀHB_4
Scrambling
products
Scheme 2. Scrambling between a single strand and a 4-
rung molecular ladder. Upon mixing of a tetrafunctional
single strand and a 4-rung molecular ladder, strand
exchange proceeds until an equilibrium mixture of single
strands and molecular ladders is afforded.
0
50
100
150
200
250
Time (h)
Figure 3. Scrambling between a tetraamine peptoid strand
and a peptoid-based, 4-rung molecular ladder. (a) MALDI
mass spectra of scrambling via transimination between E3A-
Am_4 and ME3A-HB_4 at different time points; here, HB_4s
denotes a scrambled molecular ladder composed of E3A-
Am_4 and ME3A-Al_4 strands. (b) Concentration of HB_4s
versus time during molecular ladder scrambling.
Strand exchange by transimination was examined by
utilizing a single-stranded tetraamine peptoid E3A-Am_4
in conjunction with ME3A-HB_4, a peptoid-based, 4-rung
molecular
ladder
incorporating
2-(2-(2-
methoxyethoxy)ethoxy)ethylamine (ME3A) as the spacer
residue (see Figure S16). E3A-Am_4 and ME3A-HB_4 were
added in a 1:1 stoichiometric ratio to chloroform with a
catalytic amount of scandium (III) triflate and mixed at
room temperature. Aliquots of the reaction mixture were
examined directly by MALDI mass spectrometry over the
course of 9 days to determine the rate and extent of lad-
der scrambling.
MALDI mass spectra of the tetraamine/4-rung molecu-
lar ladder reaction mixture (Figure 3(a)) demonstrate
peaks attributable to both the parent molecular ladder
ME3A-HB_4 and its scrambled product HB_4s, generated
by the transimination reaction between ME3A-HB_4 and
E3A-Am_4. As shown in Figure 3(b), this transimination-
mediated strand exchange proceeds rapidly and scram-
bling products were observed after 12 hours; indeed, the
concentration of the scrambled ladder product plateaus
after approximately 72 hours, indicating that equilibrium
is reached well within the extended reaction timeframe of
the Vernier-templated syntheses.
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Al_4 or ME3A-Am_4 and E3A-Al_4 strands. (b) Concentration
HB_4s
of HB_4s versus time during molecular ladder scrambling.
1
2
3
4
5
6
7
+
+
Sc(III)
Strand exchange via imine metathesis was also investi-
gated between 4-rung molecular ladders bearing different
spacer residues (HB_4 and ME3A-HB_4, see Scheme 3).
Using an experimental approach similar to that employed
for molecular ladder scrambling by transimination, the
molecular ladder HB_4, composed of peptoid oligomers
bearing E3A spacer residues, was mixed with ME3A-HB_4
in a 1:1 stoichiometric ratio in chloroform with a catalytic
amount of scandium (III) triflate at room temperature,
and aliquots of the reaction mixture were examined by
MALDI mass spectrometry. Although peaks attributable
to the parent molecular ladders and the scrambled prod-
uct are observable in the MALDI mass spectra of the two
4-rung molecular ladder imine metathesis reaction mix-
ture (Figure 4(a)), the product concentration is low. In-
deed, as shown in Figure 4(b), strand exchange between
molecular ladders via imine metathesis is particularly
sluggish as the concentration of the scrambled product
continues to increase even after reaction for over a week,
indicating that elimination of the out-of-registry interme-
diates generated during the Vernier assembly reaction
proceeds very slowly. Thus, the strand exchange between
molecular ladders via imine metathesis likely acts as the
rate-determining reaction for this approach to Vernier-
templated assembly.
+
HB_4
ME3AꢀHB_4
8
9
Scrambling
products
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Scheme 3. Scrambling between two different 4-rung mo-
lecular ladders. Upon mixing of the different 4-rung
molecular ladders, strand exchange proceeds until an
equilibrium mixture of molecular ladders is afforded.
HB_4 with ME3AꢀHB_4
HB_4
[M+Na]+
(a)
ME3AꢀHB_4
[M′+Na]+
HB_4s
[Ms+Na]+
t = 216 h
t = 144 h
t = 72 h
[M′+H]+ [M′+K]+
[M+H]+ [M+K]+
CONCLUSION
t = 0 h
Molecular ladders containing up to six rungs were suc-
cessfully and selectively assembled by the Sc(III)-
catalyzed dimerization of complementary, amine- and
aldehyde-bearing oligopeptoids with commensurate
lengths. Nevertheless, to curtail the kinetic trapping of
thermodynamically disfavored products inevitably result-
ing from the hybridization of sufficiently long precursor
oligomers, we utilized the Vernier-template directed, dy-
namic covalent self-assembly of oligomeric peptoids to
create large, molecular ladder structures, the lengths of
which were pre-determined by the functionalities of the
precursor strands. MALDI mass spectrometry and GPC,
performed on the reaction mixture after one week reac-
tion time, confirmed the formation of the desired ideal
molecular ladder structures in addition to the presence of
partially-assembled intermediates. Scrambling experi-
ments indicated that, whereas transimination between an
amine-bearing peptoid and a molecular ladder proceeded
rapidly, imine metathesis between two different molecu-
lar ladders had not reached equilibrium after nine days
reaction time; thus, despite the extended reaction time,
the continued presence of partially-assembled intermedi-
ates in the Vernier assembly mixture was attributed to the
slow inter-ladder imine metathesis.
2300 2400 2500 2600 2700 2800 2900
m/z
(b)
0.02
0.016
0.012
0.008
0.004
0
HB_4 with ME3AꢀHB_4
0
50
100
150
200
250
Time (h)
Figure 4. Scrambling between two different peptoid-based,
4-rung molecular ladders. (a) MALDI mass spectra of scram-
bling via imine metathesis between HB_4 and ME3A-HB_4 at
different time points; here, HB_4s denotes scrambled
molecular ladders composed either of E3A-Am_4 and ME3A-
By utilizing dynamic covalent interactions to mediate
the self-assembly of complementary sequences, we be-
lieve this approach will prove particularly suitable for the
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Journal of the American Chemical Society
(11)
Kuhn, P.; Forget, A.; Su, D. S.; Thomas, A.; Antonietti,
fabrication of multi-dimensional nanostructures with
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unparalleled thermal, chemical and mechanical stability.
Additionally, the structural diversity and sequence-
specific nature of peptoids make them excellent candi-
dates as construction media for complex nanostructures.
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MacLachlan, M. J. Pure Appl. Chem. 2006, 78, 873.
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ASSOCIATED CONTENT
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Adams, D. J.; Shakespeare, S.; Clowes, R.; Bradshaw, D.; Hasell,
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The Supporting Information is available free of charge on the
ACS Publications website.
Experimental procedures for monomer and oligomer synthe-
sis, purification, hybridization and scrambling. Oligomer and
molecular ladder characterization. (PDF)
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AUTHOR INFORMATION
Corresponding Author
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Tanoue, R.; Higuchi, R.; Enoki, N.; Miyasato, Y.;
Uemura, S.; Kimizuka, N.; Stieg, A. Z.; Gimzewski, J. K.;
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*tfscott@umich.edu
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENT
This work was supported by the U.S. Department of Energy,
Office of Science, Basic Energy Sciences, under Award # DE-
SC0012479. We thank the Thurber group and Liang Zhang
for their assistance with liquid chromatography instrumenta-
tion, Scott Zavada for his assistance with Matlab coding, and
Joseph Furgal for his assistance with NMR spectroscopy. TFS
thanks Bernard P. Scott for a lifetime of useful discussions.
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Insert Table of Contents artwork here
5
6
7
+
NH2 NH2 NH2
O
N
O
N
O
O
O
O
8
9
O
N
O
O
H2N
N
N
N
O
N
N
N
N
N
N
N
N
NH2
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
N
O
N
O
O
Sc(OTf)3/CHCl3
N
O
N
O
N
N
N
NH2
nꢀ2
O
O
O
O
O
N
N
N
N
N
N
N
N
N
N
N
N
PeptoidꢀBased Molecular Ladder
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